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Role of Asp190 in the Phosphorylation of the Antibiotic Kanamycin Catalyzed by the Aminoglycoside Phosphotransferase Enzyme: A Combined QM:QM and MD Study

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journal contribution
posted on 17.04.2020, 22:05 by Abd Al-Aziz A. Abu-Saleh, Sweta Sharma, Arpita Yadav, Raymond A. Poirier
The aminoglycoside phosphotransferase (APH(3′)-IIIa) kinases form a clinically central group of antibiotic-resistant enzymes. Computationally, we have studied the catalytic mechanism of the APH(3′)-IIIa enzyme at the atomic-level. The proposed reaction mechanism involves protonation of Asp190 by the kanamycin 3′-hydroxyl group mediated through an explicit neighboring water molecule, which leads to a simultaneous nucleophilic attack on the γ-phosphate of the ATP by the deprotonated kanamycin 3′-hydroxyl group. The second step is a proton abstraction from the protonated Asp190 to the phosphate group of the phosphorylated kanamycin mediated by an explicit water molecule. The calculated Gibbs energy of activation (ΔG) of the rate-determining step for the phosphorylation reaction is 77 kJ mol–1 at the M06-2X/6-311++G­(2df,p)//ONIOM­(M06-2X/6-31+G­(d):HF/6-31G­(d)) level of theory. This study has provided a new understanding of the APH(3′)-IIIa catalytic mechanism that agrees with the available experimental data (ΔG = 75 ± 4 kJ mol–1) and could provide a starting point for the rational design of mechanism-based inhibitors of aminoglycoside modifying enzyme to circumvent antibiotic resistance.